Breaking the Myb–KIX Alliance: Structure‐Guided Discovery of Biaryl Hydroxy‐Naphthamides as Disruptors of the c‐Myb–CBP/p300 KIX Protein–Protein Interaction
Aug 2026· Archiv der Pharmazie· Vol 359· 0 citations· 32 references
Medicine
TL;DR
3‐hydroxy‐2‐naphthamides are established as promising scaffolds for targeting the c‐Myb–CBP/p300 KIX interface and are supported as the most conformationally stable interfacial binders.
Abstract
The interaction between the transcription factor c‐Myb and the CBP/p300 KIX domain is a critical regulatory node in hematopoietic gene expression and an attractive target in MYB‐dependent leukemia. Herein, we aimed to identify new small‐molecule disruptors of the c‐Myb–CBP/p300 KIX protein–protein interaction using integrated in silico and experimental workflow. A focused library of 1143 biaryl hydroxy‐naphthamides (naphthanilides) was subjected virtual screening filters yielding five prioritized candidates (C1–C5). Docking showed that all selected compounds occupied the c‐Myb‐facing groove of the KIX domain and reproduced key interfacial contacts. Subsequent 1000 ns molecular dynamics simulations revealed distinct stability and disruption profiles, with C1 and C4 showing the most favorable combination of stable groove occupancy, protein–protein interface perturbation, and ligand‐binding energetics. Free‐energy landscape analysis further supported these compounds as the most conformationally stable interfacial binders. Differential MM/PBSA analysis of the protein–protein interface showed that C1 produced the largest predicted weakening of the c‐Myb–KIX interaction (ΔΔGPPI = +38.81 kcal/mol), followed by C4 (+29.90), C5 (+27.78), and C3 (+25.81 kcal/mol), whereas C2 was predicted to stabilize the complex (−5.41 kcal/mol). In silico ADMET profiling indicated that the series was drug‐like by Lipinski criteria but carried liabilities related to solubility, metabolism, and predicted toxicity. Experimental validation by microscale thermophoresis confirmed direct binding of the assay proteins (Kd = 26.72 ± 0.82 µM) and demonstrated that the naphthanilides disrupt the interaction in vitro. C1 was the most potent disruptor (IC50 = 9.50 ± 0.22 µM), outperforming Naphthol AS‐E phosphate (IC50 = 32.84 ± 9.46 µM). These findings establish 3‐hydroxy‐2‐naphthamides as promising scaffolds for targeting the c‐Myb–CBP/p300 KIX interface.
Findings identify Fumiquinazoline D as an early‐stage biochemical hit for disruption of the Skp2–Cks1 interaction and as a potential scaffold for further mechanistic validation and medicinal‐chemistry investigation.
Emadeldin M. Kamel, A. A. Allam, H. Rudayni et al.· ChemMedChem· 0 citations
Tingenone is identified as a promising scaffold for the development of new c-Myb-CBP/p300 KIX PPI inhibitors, having produced the clearest signatures of interfacial weakening and the most favorable disruption metrics.
Emadeldin M. Kamel, H. Rudayni, A. A. Allam et al.· Journal of Molecular Graphic...· 0 citations
Findings validate the diphenylpyrazine scaffold as a promising chemotype for Skp2–Cks1 inhibition and identify C3 as a strong lead for further optimization.
Emadeldin M. Kamel, A. A. Allam, H. Rudayni et al.· Journal of Computer-Aided Mo...· 0 citations
The interaction between c-Myb and the CBP/p300 KIX domain is a critical transcriptional regulatory event and an attractive target for the development of candidate disruptors of the recombinant c-Myb-KIX interaction. In this study, we used an integrated computational and experimental strategy to identify new small molecules capable of disrupting this protein-protein interaction. A focused Umbelliferyl phosphate scaffold library was subjected to stepwise virtual screening via drug-likeness assessment and docking to the c-Myb-binding region of the KIX domain and short molecular dynamics refinement. Selected compounds were then evaluated by 500 ns molecular dynamics simulations, MM/PBSA analysis, free energy landscape (FEL) mapping, and finally by microscale thermophoresis (MST) assay. Computational analyses showed that stable ligand binding did not necessarily translate into disruption of the c-Myb-KIX interface, allowing separation of compounds that stabilized the complex from those predicted to weaken it. Consistent with this distinction, ΔΔGPPIanalysis identified only MUP and Naphthol AS-BI phosphate as protein-protein interaction-weakening ligands, with Naphthol AS-BI phosphate showing the strongest predicted disruptive effect (ΔΔGPPI=+3.25 kcal/mol), whereas DiFMUP and Naphthol AS-D phosphate were predicted to stabilize the complex. Among the tested molecules, Naphthol AS-BI phosphate showed the clearest disruption-like behavior in silico and was the most potent inhibitor in vitro, with an IC₅₀ of 18.9 ± 0.6 μM. Importantly, MUP emerged as the most promising umbelliferyl phosphate-derived hit, displaying measurable inhibitory activity (IC₅₀ = 33.5 ± 0.3 μM) comparable to the reference Naphthol AS-E phosphate (IC₅₀ = 31.2 ± 1.3 μM) and a more favorable predicted ADMET profile. Overall, this work identifies new chemical starting points for targeting the c-Myb-CBP/p300 KIX interaction and supports MUP as an attractive scaffold for further optimization.
Emadeldin M. Kamel, H. Rudayni, A. A. Allam et al.· Biophysical Chemistry· 0 citations
The SARS‐CoV‐2 nucleocapsid (N) protein is a key regulator of viral genome packaging and replication, making it an attractive antiviral target. Here, we provide structural and energetic insights into N‐protein inhibition using molecular docking, pharmacophore screening, molecular dynamics (MD) simulations, and MM‐PBSA analyses. Experimentally known inhibitors Onalespib, JQ‐1, and Zotatifin were used to construct pharmacophores that screened the ZINC database, yielding 927 hits. Three top candidates, ZINC37602048, ZINC06246181, and ZINC12077824, underwent 150 ns MD simulations to assess their long‐term dynamic stability within the N‐protein binding pocket. MM‐PBSA calculations over the 150 ns trajectories revealed strong binding for ZINC37602048 (−27.24 kcal/mol) and ZINC06246181 (−22.81 kcal/mol), driven mainly by van der Waals contributions, whereas ZINC12077824 showed comparatively weaker, though still favorable, affinity (−18.91 kcal/mol) owing to a large unfavorable electrostatic contribution partially offset by polar solvation. These results highlight promising scaffolds for further optimization and underscore the utility of MD and free energy‐based methods in guiding antiviral drug discovery targeting the SARS‐CoV‐2 N protein.
Srimai Vuppala, Jaeyoung Kim, Mengdi Zhao et al.· Bulletin of the Korean Chemi...· 0 citations
Background: Hypoxia-inducible factor-1 alpha (HIF-1α) drives tumor adaptation to hypoxia by promoting angiogenesis, metabolic reprogramming, and survival signaling in clear cell renal cell carcinoma (ccRCC). Transcriptional activity of HIF-1α depends on its interaction with the p300/CBP (CREB-binding protein) coactivator via the C-terminal transactivation domain (C-TAD). Direct targeting of this protein–protein interface remains limited, highlighting the need for novel inhibitors.Methods: A structure-based virtual screening of ~250,000 compounds from the ZINC database was conducted to identify candidates targeting a predicted pocket within the HIF-1α C-TAD. Top hits were evaluated using molecular docking and 100 ns molecular dynamics simulations. The lead compound, HFS764, was further characterized using in silico absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling, homogeneous time-resolved fluorescence (HTRF) assays, and differential scanning fluorimetry (DSF). Functional effects were assessed in Caki-1 cells under hypoxia using hypoxia response element (HRE)-luciferase assays, cell viability and vascular endothelial growth factor (VEGF) secretion.Results: HFS764 demonstrated stable binding within the HIF-1α pocket, with ligand root-mean-square deviation (RMSD) <0.20 nm and a predicted binding free energy of –22.38 kcal/mol. HTRF assays confirmed inhibition of the HIF-1α–p300 interaction (IC50 = 4.89 μM), while DSF showed ligand-induced stabilization (ΔTm = +2.0 °C). In Caki-1 cells, HFS764 suppressed HRE-driven transcription (IC50 = 4.27 μM), and reduced VEGF secretion under hypoxia. Selective cytotoxicity was observed (GI50: 14.70 μM in Caki-1 vs. 37.98 μM in HK-2; therapeutic index = 2.58).Conclusion: HFS764 disrupts the HIF-1α–p300 interface and suppresses hypoxia-driven signaling in ccRCC, supporting the use of transcriptional complex inhibition as a promising therapeutic strategy.
Mesfer Al Shahrani· Discover medicine· 0 citations
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